Reassessing taxonomy and virulence in the group-rebuttal of clades " C1" and " C2," genome announcement for and description of sp. nov.

UNLABELLED

There is a considerable interest in the association between and colorectal cancer (CRC). Recently, it was suggested that this association is valid only for a distinct clade of ( C2) and that strains belonging to another clade ( C1) are only associated with the oral cavity. It was further suggested that this made C1 a natural comparator when looking for candidate genes associated with the pathogenicity of C2. Based on such comparisons, three candidate operons enriched in CRC were suggested to explain the strong association of colorectal tumor with . In the present paper, we show that major taxonomic errors invalidate the existence of two distinct clades of and that C1 is simply a rediscovery and misclassification of . We further reassess the phylogenetic structure of the entire group encompassing and all known closely related species and confirm the current taxonomy using contemporary phylogenetic principles. We also describe a novel species more closely related to than any other known species, for which we propose the name sp. nov. We further searched for the three proposed candidate virulence operons of across the entire group and show that some or all of these are present in all other species except . We also observe considerable variability of Type V secretion systems (T5SS) by subtype and abundance across the group.

IMPORTANCE

Considerable resources are being used to study associations between the human microbiota and malignancy. There is a particular interest in the connection between and colorectal cancer. In this paper, we correct recent taxonomic misconceptions of importance to this research and critically reassess proposed gene candidates for explaining pathogenicity. We demonstrate the importance of strict adherence to taxonomic rules when discovering possibly novel phylogenetic groups and emphasize that genome references are still not available for all known bacteria. We reassess the phylogeny of the medically important group including using contemporary approaches, provide a genome reference for and describe sp. nov. Our results dispute the concept of using a single closely related comparator phylogenetic group when searching for candidate genes potentially explaining species-specific pathogenicity and show that such comparative approaches can only be meaningful when all relevant related species are included.